“I wonder how you say ‘amphilicite’ in Mandarin.”

Alt-Astrid: Excuse me, agents. Have you seen Col. Broyles? He’s late to work this morning.
Lincoln: Have you tried calling him?
Alt-Astrid: Yes, I’d tried calling him. At home too. And his wife said that he did not come home last night and that is very unlike him.

Entrada - Fringe, Season 3, Episode 8

Alt-Astrid: Agents. I’ve been asking around, no one has seen Col. Broyles come in today. I checked and his subcutaneous tracker was disabled two hours ago. Should we be worried?

The Consultant - Fringe, Season 4, Episode 18

Alt!Astrid: I don’t like funerals. I never know what I’m supposed to say.
Agent Lee: There’s nothing you can say.

The One Where Agent Lee Wants All The Olivias

Capt Lee: I wish I was told sooner.
Walternate: You weren’t told because it was classified.
Bloodline - Fringe, Season 3, Episode 18

Walternate: It’s come all too clear that elements of our government are being infiltrated.
Back To Where You’ve Never Been - Fringe, Season 4, Episode 8

Liv:The Secretary’s son. He’s cute, huh? Bet he’s all contradictory and tricky like his dad.
Making Angels - Fringe, Season 4, Episode 11

Capt Lee: Who knew?
Agent Lee: What?
Capt Lee: Who else knew we were transporting him?
Everything In Its Right Place - Fringe, Season 4 Episode 17

Theory Time
Maybe Capt Lee is alive. At the end there he knew something was up, and maybe he became suspicious of our!Linc (afterall, the shapeshifter didn’t kill him), and though maybe he still trusted Liv, he couldn’t really talk to her because they weren’t alone, and he was too busy dying.

Maybe when he got to the hospital - he was fixed, but the Secretary, having become suspicious/aware that there’s a significant leak in the FD sets him on an extra classified mission to find out who. A mission he can only complete if he pretends to be dead.

(I don’t know where to fit Nick Lane into this. But he’s mixed up in it somehow.)

Or, he really could be dead.